Publications

Peer-Reviewed Articles

1. Mechanical deformation affects the condensation of counterions in highly swollen polyelectrolyte hydrogels. M. Rafique & A. Erbas, Soft Matter (2023). DOI: 10.1039/D3SM00585B
2. Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization,  J. Paturej & A. Erbas, Phys. Biology (2023). DOI: 10.1088/1478-3975/ace750
3. Hydrogel-integrated optical fiber sensors and their applications: A comprehensive review.  Sadeque et al. J. Materials Chem. C (2023) DOI: 10.1039/D3TC01206A
4. Effect of Charge State on the Equilibrium and Kinetic Properties of Mechanically Interlocked [5]Rotaxane: A Molecular Dynamics Study. A. U. Özkan, D. Tuncel & A. Erbaş, J. Phys. Chem. B (2023). DOI: 10.1021/acs.jpcb.2c07645
5. Facilitated Dissociation of Nucleoid Associated Proteins in the Bacterial Confinement (cover issue). Z. Koşar, A.G. Attar, and A. Erbaş, Biophysical J., (2022). DOI: 10.1101/2021.03.11.434965
6. Can the Concentration of a Transcription Factor Affect Gene Expression? Z. Koşar and A. Erbaş,
   Frontiers in Soft Matter (2022). DOI: 10.3389/frsfm.2022.914494
7. Interactions Between Densely Grafted Molten Polymer Brushes:  Scaling theories versus molecular simulations. A. Erbaş, Turkish J. Physics (2021). DOI:10.3906/fiz-2010-5
8. Chromophore Amphiphile-Polyelectrolyte Hybrid Hydrogels for Photocatalytic Hydrogen Production.
   H. Sai, A. Erbaş, A. Dannenhoffer, D. Huang, A, Weingarten, Z. A. Pinto, E. Siismets, K. Jang, K. Qu, M. O. de la Cruz, S. I. Stupp, J. Material. Chem. A (2020). DOI: 10.1039/C9TA08974H3
9. How Do DNA-Bound Proteins Leave their Binding Sites? Role of facilitated dissociation.
   A. Erbaş, J. F. Marko, Current Opinion in Chem. Bio. (2019). DOI: 10.1016/j.cbpa.2019.08.007
10. Rebinding Kinetics of Ligand Particles in Confinement
    A. Erbaş, M. O. de la Cruz, J. F. Marko, Biophysical J. (2019). DOI:10.1016/j.bpj.2019.02.033
11. Effects of Electrostatic Interactions on Ligand Dissociation Kinetics
    A. Erbaş, M. O. de la Cruz, J. F. Marko, Phys. Rev. E (2018) DOI:10.1103/PhysRevE.97.022405
12. Co-Assembly of Peptide Amphiphiles and Lipids into Supramolecular Nanostructures Driven by Anion-π Interactions. Z. Yu, A. Erbaş, F. Tantakitti, L. C. Palmer, J. A. Jackman, M. O. de la Cruz, N. Cho, S. I. Stupp, J. Am. Chem. Soc. (2017). DOI:10.1021/jacs.7b02058
13. Facilitated Dissociation of Transcription Factors from Single DNA Binding Sites
    R. I. Kamar, E. J. Banigan, A. Erbaş, R. D. Giuntoli, M. Olvera de la Cruz, R. C. Johnson, J. F. Marko,
    Proc. Natl. Acad. Sci. U.S.A. (2017). DOI:10.1073/pnas.1701884114
14. Ionic Conductivity in Polyelectrolyte Hydrogels, H. Li, A. Erbaş, J. Zwanikken, M. O. de la Cruz, Macromolecules (2016). DOI: 10.1021/acs.macromol.6b01276
15. Interactions between Polyelectrolyte Gel Surfaces, A. Erbaş, M. O. de la Cruz,
    Macromolecules (2016). DOI: 10.1021/acs.macromol.6b01416
16. Morphology-Induced Conductivity in Dry Ionic Liquid,  A. Erbas, M. Olvera de la Cruz,
    Phys. Chem. Chem. Phys.  (2016).  DOI: 10.1039/C5CP07090B
17. Energy Conversion in Polyelectrolyte Hydrogels, A. Erbas, M. Olvera de la Cruz,
    ACS Macro Letters  (2015). DOI:10.1021/acsmacrolett.5b00363 (cover issue),
18. Friction between Ring-Polymer Brushes, A. Erbas, J. Paturej,
    Soft Matter  (2015). DOI: 10.1039/C4SM02818J
19. Detachment of Semiflexible Polymer Chains from a Substrate – a Molecular Dynamics investigation, J. Paturej, A. Erbas, A. Milchev, V.G. Rostiashvili,
    J. Chem. Phys. 141, 22, (2014). DOI: 10.1063/1.4902551
20. Confinement-Dependent Friction in Peptide-Bundles, A. Erbas and R. R. Netz,
    Biophysical J. 104, 6, (2013).  DOI: 10.1016/j.bpj.2013.02.008
21. Viscous Friction of Hydrogen-Bonded Matter, A. Erbas, D. Horinek and R. R. Netz,
    J. Am. Chem. Soc. 134 , pp 623 (2012). DOI: 10.1021/ja209454a
22. Viscous Compressible Hydrodynamics at Planes, Spheres and Cylinders with Finite Surface Slip (cover issue), A. Erbas, R. Podgornik and R. R. Netz,
    Euro. Phys. E 32, pp 147 (2010). DOI: 10.1140/epje/i2010-10610-7
23. Phase Diagrams and Crossover in Spatially Anisotropic d=3 Ising, XY Magnetic, and Percolation Systems: Exact Renormalization – Group Solutions of Hierarchical Models,
    A. Erbas, A. Tuncer, B. Yücesoy, and A. N. Berker,
    Phys. Rev. E 72, 026129 (2005).  DOI: 10.1103/PhysRevE.72.026129
    

Preprints (available on public repositories)

• Molecular Rheology of Nanoconfined Polymer Melts, A. B. Yıldırım, A Erbaş, L Biancofiore, arXiv e-prints, arXiv: 2303.09178
• Heterochromatin flexibility contributes to chromosome segregation in the cell nucleus (2020), M. Girard, M.O. de la Cruz, J.F. Marko, and A. Erbaş, @BioRxiv.org, DOI:https://doi.org/10.1101/2020.12.01.403832 

• Darya Karimpour, MSc Thesis.  Molecular Dynamics Simulations of surface-grafted co-polymers. (Adv: Aykut Erbas).
• Ata Utku Özkan, MSc Thesis.  Molecular Dynamics Simulations Study of [5]Rotaxane  in Bulk and at Interfaces. (Adv: Aykut Erbas). Abstract: English.
• Zafer Koşar, MSc Thesis. Protein-DNA dissociation kinetics and chromosome organization in a model bacterial confinement (Adv: Aykut Erbas). Abstract: English.
• Aykut Erbaş, PhD Thesis. Friction of Soft Matter at  the  Nano-Scale  (Adv:Roland R. Netz). Abstract: English, German, Turkish
• Aykut Erbaş, MSc Thesis. Two Statistical Physics Problems: Phase Diagram Calculation of Spatially Anisotropic, Surfaced d= 3 Layered Systems by Renormalization-Group Theory and Vehicle-Route Optimization with Traffic Factors for Migros Home Delivery System by Simulated Annealing  (Adv: A. Nihat Berker). Abstract: English, Turkish
• Aykut Erbaş, BSc Thesis. Heat Capacity of Hierarchical Ising Lattices   (Adv: A. Nihat Berker). Abstract: English, Turkish

Journal covers